相关论文: Efficient Construction of the BWT for Repetitive T…

Bidirectional compression algorithms work by substituting repeated substrings by references that, unlike in the famous LZ77-scheme, can point to either direction. We present such an algorithm that is particularly suited for an external…

In this paper, we show that the LZ77 factorization of a text T {\in\Sigma^n} can be computed in O(R log n) bits of working space and O(n log R) time, R being the number of runs in the Burrows-Wheeler transform of T reversed. For extremely…

In this paper we study the number $r_{bwt}$ of equal-letter runs produced by the Burrows-Wheeler transform ($BWT$) when it is applied to purely morphic finite words, which are words generated by iterating prolongable morphisms. Such a…

The Burrows-Wheeler Transform (BWT) of a string is an invertible permutation of the string, which can be used for data compression and compact indexes for string pattern matching. Ganguly et al. [SODA, 2017] introduced the parameterized BWT…

Retrieval augmentation addresses many critical problems in large language models such as hallucination, staleness, and privacy leaks. However, running retrieval-augmented language models (LMs) is slow and difficult to scale due to…

We propose a novel approach to reduce memory consumption of the backpropagation through time (BPTT) algorithm when training recurrent neural networks (RNNs). Our approach uses dynamic programming to balance a trade-off between caching of…

Compression algorithms and streaming algorithms are both powerful tools for dealing with massive data sets, but many of the best compression algorithms -- e.g., those based on the Burrows-Wheeler Transform -- at first seem incompatible with…

A weight based dynamic compression method has recently been proposed, which is especially suitable for the encoding of files with locally skewed distributions. Its main idea is to assign larger weights to closer to be encoded symbols by…

The positional Burrows-Wheeler Transform (PBWT) is commonly used to store haplotype panels compactly in such a way that, given a query haplotype, we can quickly find the set maximal exact matches (SMEMs) between the query and the haplotypes…

We survey the different methods used for extending the BWT to collections of strings, following largely [Cenzato and Lipt\'ak, CPM 2022, Bioinformatics 2024]. We analyze the specific aspects and combinatorial properties of the resulting BWT…

Until recently, most experts would probably have agreed we cannot backwards-step in constant time with a run-length compressed Burrows-Wheeler Transform (RLBWT), since doing so relies on rank queries on sparse bitvectors and those inherit…

Parameterized strings are a generalization of strings in that their characters are drawn from two different alphabets, where one is considered to be the alphabet of static characters and the other to be the alphabet of parameter characters.…

Long-term location tracking, where trajectory compression is commonly used, has gained high interest for many applications in transport, ecology, and wearable computing. However, state-of-the-art compression methods involve high space-time…

The longest common prefix array is a very advantageous data structure that, combined with the suffix array and the Burrows-Wheeler transform, allows to efficiently compute some combinatorial properties of a string useful in several…

A standard format used for storing the output of high-throughput sequencing experiments is the FASTQ format. It comprises three main components: (i) headers, (ii) bases (nucleotide sequences), and (iii) quality scores. FASTQ files are…

Recently, Cenzato et al.\ proposed a new text index, called the \emph{suffixient array}, which is a subset of the suffix array and supports locating a single pattern occurrence or finding its maximal exact matches (MEMs), assuming random…

In this paper we investigate the problem of partitioning an input string T in such a way that compressing individually its parts via a base-compressor C gets a compressed output that is shorter than applying C over the entire T at once.…

With the popularity of the recent Transformer-based models represented by BERT, GPT-3 and ChatGPT, there has been state-of-the-art performance in a range of natural language processing tasks. However, the massive computations, huge memory…

Prior work inspired by compression algorithms has described how the Burrows Wheeler Transform can be used to create a distance measure for bioinformatics problems. We describe issues with this approach that were not widely known, and…

In this paper, we describe a new type of match between a pattern and a text that aren't necessarily maximal in the query, but still contain useful matching information: locally maximal exact matches (LEMs). There are usually a large amount…